-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I think in this case though that this is the cause of the user not seeing any results?
Syed Haider wrote: > I am confused. > > (To SYED...: do you have any ideas? MartView/MartService on this user's > own server is throwing exceptions like this: Can't open a reference at > <blah blah>/lib/BioMart/Web.pm line 1850.) > > >> Yeah, I know whats this all about. Its a warning not causing any harm due >> passing a string to a file which sometimes is not assigned a value. Will >> be fixed soon. I dont sense if this should cause any serious troubles. >> Cheers >> Syed > > > > cheers, > Richard > > Etai Jacob wrote: >>>> Yes we have, the last version:( >>>> >>>> On 2/13/07, Richard Holland <[EMAIL PROTECTED]> wrote: >>>> Hmm. Well it must be a CPAN module then... not sure exactly as I've not >>>> seen this problem before. The line I quoted is definitely the line that >>>> is causing your results to be blank though. >>>> >>>> You could check to see if you have IO::Stringy installed from CPAN. It >>>> provides the functions that back up the open() method. Let me know if it >>>> is installed or not - if not, install it and retry the request (you'll >>>> have to restart the MartView server after installing it). >>>> >>>> cheers, >>>> Richard >>>> >>>> Etai Jacob wrote: >>>>> We have perl 5.85 installed. >>>>> Thanks, >>>>> Etai >>>>> On 2/13/07, Richard Holland <[EMAIL PROTECTED]> wrote: >>>>> This line of the log indicates the problem: >>>>> Can't open a reference at >>>>> /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web.pm line 1850. >>>>> This is a Perl version incompatibility. It is trying to open a >>>>> filehandle over a string then write the results to that string. This is >>>>> not possible in versions of Perl older than 5.8. >>>>> You need to upgrade your Perl to at least 5.8 for this to work. >>>>> cheers, >>>>> Richard >>>>> Etai Jacob wrote: >>>>>> Attached. >>>>>> On 2/13/07, Arek Kasprzyk <[EMAIL PROTECTED]> wrote: >>>>>>> On 13 Feb 2007, at 11:49, Etai Jacob wrote: >>>>>>>> No errors. >>>> >>>>>>> I meant ... could you send us the contents >>>>>>> of this file while you are doing your query? >>>>>>> we need to see what comes back from the >>>>>>> database or webserver when you do it >>>> >>>>>>> cheers, >>>>>>> a. >>>> >>>> >>>> >>>>>>>> On 2/13/07, Arek Kasprzyk <[EMAIL PROTECTED]> wrote: >>>>>>>>> On 13 Feb 2007, at 11:23, Etai Jacob wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> My answers below. >>>>>>>>> Hi Etai, >>>>>>>>> maybe we need a little bit more debugging there. >>>>>>>>> Could you change the >>>>>>>>> >>>>>>>>> log4perl.threshold = FATAL >>>>>>>>> >>>>>>>>> to >>>>>>>>> >>>>>>>>> log4perl.threshold = WARN >>>>>>>>> >>>>>>>>> in biomart-perl/conf/log4perl.conf >>>>>>>>> >>>>>>>>> restart the server and see what you get >>>>>>>>> in the error_log? >>>>>>>>> >>>>>>>>> >>>>>>>>> cheers, >>>>>>>>> a. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>>> What do you mean by not seeing any results? Do you mean that >>>> you >>>>>>>>> get >>>>>>>>>>> an error message? >>>>>>>>>> I don't get any error messages, not on the web browser >>>>> (firefox or >>>>>>>>>> explorer) and not in the error log file of the httpd. >>>>>>>>>> >>>>>>>>>> Or you see the results page but the table only has >>>>>>>>>>> headings? >>>>>>>>>> No heading. >>>>>>>>>> >>>>>>>>>> What happens exactly? >>>>>>>>>> When pressing the "results" it waits a second and then when >>>>> "Done" >>>>>>>>> the >>>>>>>>>> page stays blank (except the default GUI of the martview on >>>>> the left >>>>>>>>>> side of the page). >>>>>>>>>> >>>>>>>>>>> Could you try a query with no filters at all and just one or >>>> two >>>>>>>>>>> attributes to see if you get results? >>>>>>>>>> Yes I tried with many combinations. Nothing. >>>>>>>>>> >>>>>>>>>> I tried other biomart web interface, >>>>>>>>>> http://www.dictybase.org/biomart/martview/, to see whether I >>>>> have a >>>>>>>>>> problem with the browser or JVM but it works fine. >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Etai >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> Etai Jacob wrote: >>>>>>>>>>>> Hi, >>>>>>>>>>>> >>>>>>>>>>>> I am trying to execute few basic queries using the biomart >>>> web >>>>>>>>>>>> interface with the default configurations (as instructed in >>>>> the >>>>>>>>>>>> installation guide). >>>>>>>>>>>> I don't get to see any results on the browser even though >>>>> at the >>>>>>>>>>> count >>>>>>>>>>>> stage I see that there are relevant entries (i.e. 1/3967). >>>>>>>>>>>> >>>>>>>>>>>> What could be the problem? >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Etai >>>>>>>>>>>> >>>> >>>> >> > ====================================== > Syed Haider. > EMBL-European Bioinformatics Institute > Wellcome Trust Genome Campus, Hinxton, > Cambridge CB10 1SD, UK. > ====================================== -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFF0tAV4C5LeMEKA/QRAlx0AJ9CWHlRwxfcEOkklOfHxRsnaJDNyACeK6as FKa6LW0dRQtxk6hKD9UmkQ4= =jTFK -----END PGP SIGNATURE-----
